Browse reusable Agent Skills, each with a clear purpose and practical guidance.
Load when computing genome-assembly QC metrics — N50/N90, L50/L90, total length, contig count, GC content, longest-contig — from a FASTA produced by any assembler (SPAdes / Megahit / Flye / Canu). Skip when running the assembly itself or when assessing alignment quality (use `genomics-alignment`).
Load when summarising a peak file (BED / narrowPeak) from ATAC-seq / ChIP-seq / CUT&Tag — peak count, width distribution, per-chromosome counts, score statistics. Skip when calling peaks from BAM (run MACS / Genrich externally first) or when working with single-cell ATAC (use `scatac-preprocessing`).
Load when summarising small variants (SNVs / indels) from a VCF or computing demo-pattern variant statistics (Ti/Tv ratio, per-chromosome distribution, SNP / indel split). Skip when filtering / merging VCFs (use `genomics-vcf-operations`), when calling structural variants (use `genomics-sv-detection`), or when adding functional annotations (use `genomics-variant-annotation`).
Load when extracting GEO accessions, dataset metadata, and downloadable references from a scientific paper (PDF / URL / DOI / PubMed ID / raw text) for downstream omics analysis. Skip when the dataset is already in hand or when only routing a query (use `orchestrator`).
Load when running two-group metabolomics DE (t-test + log2FC + BH-FDR + PCA) on a feature × sample CSV using `--group-a-prefix` / `--group-b-prefix` (default `ctrl` / `treat`). Skip when needing tunable test backends (use `metabolomics-statistics` for Wilcoxon / ANOVA / Kruskal) or for raw spectra.
Load when normalising a feature × sample metabolomics CSV via median, quantile, total (sum), PQN (probabilistic quotient), or log methods — emits a normalised wide-form table. Skip when also imputing (use `metabolomics-quantification`) or for raw spectra (run `metabolomics-xcms-preprocessing` first).
Load when imputing missing values (min / median / KNN) and normalising (TIC / median / log) a feature × sample metabolomics CSV. Skip when only normalisation is needed (use `metabolomics-normalization`) or when the input is raw spectra (run `metabolomics-xcms-preprocessing` first).
Load when running univariate two-group testing (t-test / Wilcoxon / ANOVA / Kruskal-Wallis) on a feature × sample metabolomics CSV with `--group1-prefix` / `--group2-prefix` column matching, BH-FDR adjusted. Skip when working with raw spectra (run `metabolomics-xcms-preprocessing`) or for two-group DE with default `ctrl` / `treat` prefixes (use `metabolomics-de`).
Load when running an XCMS-style preprocessing summary on LC-MS metabolomics raw / vendor-converted files — emits a peak table with m/z, retention time, and per-sample intensities. Skip when working with an already-built peak table (use `metabolomics-peak-detection`) or when only annotation is needed (use `metabolomics-annotation`).
Load when ingesting a MaxQuant `proteinGroups.txt`, FragPipe `combined_protein.tsv`, DIA-NN report, or generic CSV / TSV protein-quantification table — normalises columns to a standard schema, emits `tables/proteins.csv`. Skip when raw spectra are the input (run the search engine first) or when the file is already OmicsClaw schema.